tbuckley/cabot-search huggingface dataset:
Genome-wide association study of placental weight identifies distinct and shared genetic influences between placental and fetal growth
Authors: Robin N. Beaumont, Christopher Flatley, Marc Vaudel, Xiaoping Wu, Jing Chen, Gunn-Helen Moen, Line Skotte, Øyvind Helgeland, Pol Solé-Navais, Karina Banasik, Clara Albiñana, Justiina Ronkainen, João Fadista, Sara Elizabeth Stinson, Katerina Trajanoska, Carol A. Wang, David Westergaard, Sundararajan Srinivasan, Carlos Sánchez-Soriano, Jose Ramon Bilbao, Catherine Allard, Marika Groleau, Teemu Kuulasmaa, Daniel J. Leirer, Frédérique White, Pierre-Étienne Jacques, Haoxiang Cheng, Ke Hao, Ole A. Andreassen, Bjørn Olav Åsvold, Mustafa Atalay, Laxmi Bhatta, Luigi Bouchard, Ben Michael Brumpton, Søren Brunak, Jonas Bybjerg-Grauholm, Cathrine Ebbing, Paul Elliott, Line Engelbrechtsen, Christian Erikstrup, Marisa Estarlich, Stephen Franks, Romy Gaillard, Frank Geller, Jakob Grove, David M. Hougaard, Eero Kajantie, Camilla S. Morgen, Ellen A. Nohr, Mette Nyegaard, Colin N. A. Palmer, Ole Birger Pedersen, Fernando Rivadeneira, Sylvain Sebert, Beverley M. Shields, Camilla Stoltenberg, Ida Surakka, Lise Wegner Thørner, Henrik Ullum, Marja Vaarasmaki, Bjarni J. Vilhjalmsson, Cristen J. Willer, Timo A. Lakka, Dorte Gybel-Brask, Mariona Bustamante, Torben Hansen, Ewan R. Pearson, Rebecca M. Reynolds, Sisse R. Ostrowski, Craig E. Pennell, Vincent W. V. Jaddoe, Janine F. Felix, Andrew T. Hattersley, Mads Melbye, Deborah A. Lawlor, Kristian Hveem, Thomas Werge, Henriette Svarre Nielsen, Per Magnus, David M. Evans, Bo Jacobsson, Marjo-Riitta Järvelin, Ge Zhang, Marie-France Hivert, Stefan Johansson, Rachel M. Freathy, Bjarke Feenstra, Pål R. Njølstad
Journal: Nature Genetics (2023)

Abstract A well-functioning placenta is essential for fetal and maternal health throughout pregnancy. Using placental weight as a proxy for placental growth, we report genome-wide association analyses in the fetal ( n = 65,405), maternal ( n = 61,228) and paternal ( n = 52,392) genomes, yielding 40 independent association signals. Twenty-six signals are classified as fetal, four maternal and three fetal and maternal. A maternal parent-of-origin effect is seen near KCNQ1 . Genetic correlation and colocalization analyses reveal overlap with birth weight genetics, but 12 loci are classified as predominantly or only affecting placental weight, with connections to placental development and morphology, and transport of antibodies and amino acids. Mendelian randomization analyses indicate that fetal genetically mediated higher placental weight is causally associated with preeclampsia risk and shorter gestational duration. Moreover, these analyses support the role of fetal insulin in regulating placental weight, providing a key link between fetal and placental growth.
Spatially resolved metabolomics and isotope tracing reveal dynamic metabolic responses of dentate granule neurons with acute stimulation
Authors: Anne Miller, Elisa M. York, Sylwia A. Stopka, Juan Ramón Martínez-François, Md Amin Hossain, Gerard Baquer, Michael S. Regan, Nathalie Y. R. Agar, Gary Yellen
Journal: Nature Metabolism (2023)
Disparities in COVID-19 Vaccination Status Among Long-Term Care Facility Residents — United States, October 31, 2022–May 7, 2023
Authors: Emily Haanschoten, Heather Dubendris, Hannah E. Reses, Kira Barbre, Lu Meng, Andrea Benin, Jeneita M. Bell
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Residents of long-term care (LTC) facilities constitute a population that is vulnerable to SARS-CoV-2 infection; COVID-19 vaccination effectively reduces severe COVID-19 in these settings. To examine demographic differences in primary and up-to-date vaccination status against COVID-19 among LTC facility residents, a descriptive analysis of COVID-19 vaccination data from the National Healthcare Safety Network (NHSN) COVID-19 vaccination data from October 31, 2022, to May 7, 2023, were analyzed. Being up to date was defined as having received a bivalent COVID-19 vaccine dose or having completed a primary vaccination series <2 months earlier. Geographic disparities in vaccination coverage were identified, with substantially lower prevalences of up-to-date status among LTC facility residents in the South (Region 6) (37.7%) and Southeast (Region 4) (36.5%) than among those in the Pacific Northwest (Region 10) (53.3%) and Mountain West (Region 8) (59.6%) U.S. Department of Health and Human Services regions. Up-to-date status was lowest among Black or African American (39.9%) and multiracial (42.2%) LTC facility residents. Strategies to increase up-to-date COVID-19 vaccination among LTC facility residents could include and address these geographic and racial differences.
Heterogeneity and Utility of Pharmaceutical Company Sharing of Individual-Participant Data Packages
Authors: Ashley M. Hopkins, Natansh D. Modi, Ahmad Y. Abuhelwa, Ganessan Kichenadasse, Nicole M. Kuderer, Gary H. Lyman, Michael D. Wiese, Ross A. McKinnon, Frank W. Rockhold, Aaron Mann, Andrew Rowland, Michael J. Sorich
Journal: JAMA Oncology (2023)

The pharmaceutical industry has made substantial investments in developing processes for sharing individual-participant data (IPD) from clinical trials. However, the utility and completeness of shared IPD and supporting documents must be evaluated to ensure the potential for scientific advancements from the data sharing ecosystem can be realized.To assess the utility and completeness of IPD and supporting documents provided from industry-sponsored clinical trials.From February 9, 2022, to February 9, 2023, 91 of 203 clinical trials supporting US Food and Drug Administration registrations of anticancer medicines for the treatment of solid tumors from the past decade were confirmed as eligible for IPD request. This quality improvement study performed a retrospective audit of the utility and completeness of the IPD and supporting documents provided from the 91 clinical trials for a planned meta-analysis.Request for IPD from 91 clinical oncology trials indicated as eligible for the request.The utility and completeness of the IPD and supporting documents provided.The IPD packages were obtained from 70 of 91 requested clinical trials (77%). The median time to data provision was 123 (range, 117-352) days. Redactions were observed in 18 of the acquired IPD packages (26%) for outcome data, 11 (16%) for assessment variables, and 19 (27%) for adjustment data. Additionally, 20 IPD packages (29%) lacked a clinical study report, 4 (6%) had incomplete or missing data dictionaries, and 20 (29%) were missing anonymization or redaction description files. Access to IPD from 21 eligible trials (23%) was not granted.In this quality improvement study, there was substantial variability within the provided IPD packages regarding the completeness of key data variables and supporting documents. To improve the data sharing ecosystem, key areas for enhancement include (1) ensuring that clinical trials are eligible for IPD sharing, (2) making eligible IPD transparently accessible, and (3) ensuring that IPD packages meet a standard of utility and completeness.
On Enhancing Clinical Trial Data Sharing
Authors: Marc Buyse
Journal: JAMA Oncology (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
High accuracy of a blood ctDNA-based multimodal test to detect colorectal cancer
Authors: X. Bessa, J. Vidal, J.C. Balboa, C. Márquez, S. Duenwald, Y. He, V. Raymond, I. Faull, A. Burón, C. Álvarez-Urturi, X. Castells, B. Bellosillo, C. Montagut
Journal: Annals of Oncology (2023)

Detection of circulating tumor DNA (ctDNA) is a minimally invasive and convenient blood-based screening strategy that may increase effectiveness of colorectal cancer (CRC) screening.A novel multimodal ctDNA-based blood assay that integrates genomics, epigenomics and fragmentomics, as well as proteomics in a refined version, was tested in blood samples from two cohorts: (i) consecutive fecal immunochemical test (FIT)-positive individuals from the CRC Barcelona stool-based screening program; (ii) patients diagnosed with CRC. Primary endpoint was the performance of the test to detect CRC at different tumor-node-metastasis (TNM) stages. Secondary endpoint was the ability of the test to detect advanced precancerous lesions (advanced adenoma or advanced serrated lesion).A total of 623 blood samples were analyzed in the primary analysis. Sensitivity and specificity of the assay to detect CRC was 93% and 90%, respectively. The sensitivity of CRC detection according to TNM stages was 84% for stage I, 94% for stage II and 96% for stage III (70/73) (P< 0.024). Sensitivity to detect advanced precancerous lesions was 23% with a refined version of the test (including protein and updating bioinformatic thresholding).A blood-based multimodal ctDNA assay detected CRC with high accuracy. This minimally invasive, accessible and convenient assay may help to increase the effectiveness of CRC screening.
Single-cell mapping identifies MSI+ cells as a common origin for diverse subtypes of pancreatic cancer
Authors: Nirakar Rajbhandari, Michael Hamilton, Cynthia M. Quintero, L. Paige Ferguson, Raymond Fox, Christian M. Schürch, Jun Wang, Mari Nakamura, Nikki K. Lytle, Matthew McDermott, Emily Diaz, Hannah Pettit, Marcie Kritzik, Haiyong Han, Derek Cridebring, Kwun Wah Wen, Susan Tsai, Michael G. Goggins, Andrew M. Lowy, Robert J. Wechsler-Reya, Daniel D. Von Hoff, Aaron M. Newman, Tannishtha Reya
Journal: Cancer Cell (2023)
Corrigendum to “Ultrasound-triggered piezocatalytic composite hydrogels for promoting bacterial-infected wound healing” [Bioact. Mater. 24 (2023) 96–111]
Authors: Dun Liu, Lei Li, Ben-Long Shi, Bo Shi, Ming-Ding Li, Yong Qiu, Di Zhao, QunDong Shen, Ze-Zhang Zhu
Journal: Bioactive Materials (2023)

[This corrects the article DOI: 10.1016/j.bioactmat.2022.11.023.].
Postpartum defects in inflammatory response after gestational diabetes precede progression to type 2 diabetes: a nested case-control study within the SWIFT study
Authors: Julie A.D. Van, Yihan Luo, Jayne S. Danska, Feihan Dai, Stacey E. Alexeeff, Erica P. Gunderson, Hannes Rost, Michael B. Wheeler
Journal: Metabolism (2023)

BackgroundGestational diabetes (GDM) is a distinctive form of diabetes that first presents in pregnancy. While most women return to normoglycemia after delivery, they are nearly ten times more likely to develop type 2 diabetes than women with uncomplicated pregnancies. Current prevention strategies remain limited due to our incomplete understanding of the early underpinnings of progression.AimTo comprehensively characterize the postpartum profiles of women shortly after a GDM pregnancy and identify key mechanisms responsible for the progression to overt type 2 diabetes using multi-dimensional approaches.MethodsWe conducted a nested case-control study of 200 women from the Study of Women, Infant Feeding and Type 2 Diabetes After GDM Pregnancy (SWIFT) to examine biochemical, proteomic, metabolomic, and lipidomic profiles at 6–9 weeks postpartum (baseline) after a GDM pregnancy. At baseline and annually up to two years, SWIFT administered research 2-h 75-g oral glucose tolerance tests. Women who developed incident type 2 diabetes within four years of delivery (incident case group, n = 100) were pair-matched by age, race, and pre-pregnancy body mass index to those who remained free of diabetes for at least 8 years (control group, n = 100). Correlation analyses were used to assess and integrate relationships across profiling platforms.ResultsAt baseline, all 200 women were free of diabetes. The case group was more likely to present with dysglycemia (e.g., impaired fasting glucose levels, glucose tolerance, or both). We also detected differences between groups across all omic platforms. Notably, protein profiles revealed an underlying inflammatory response with perturbations in protease inhibitors, coagulation components, extracellular matrix components, and lipoproteins, whereas metabolite and lipid profiles implicated disturbances in amino acids and triglycerides at individual and class levels with future progression. We identified significant correlations between profile features and fasting plasma insulin levels, but not with fasting glucose levels. Additionally, specific cross-omic relationships, particularly among proteins and lipids, were accentuated or activated in the case group but not the control group.ConclusionsOverall, we applied orthogonal, complementary profiling techniques to uncover an inflammatory response linked to elevated triglyceride levels shortly after a GDM pregnancy, which is more pronounced in women who progress to overt diabetes.
Incidence and predictors of hepatocellular carcinoma in patients with autoimmune hepatitis
Authors: Francesca Colapietro, Patrick Maisonneuve, Ellina Lytvyak, Ulrich Beuers, Robert C. Verdonk, Adriaan J. van der Meer, Bart van Hoek, Sjoerd D. Kuiken, Johannes T. Brouwer, Paolo Muratori, Alessio Aghemo, Francesco Carella, Ad P. van den Berg, Kalliopi Zachou, George N. Dalekos, Daniel E. Di Zeo-Sánchez, Mercedes Robles, Raul J. Andrade, Aldo J. Montano-Loza, Floris F. van den Brand, Charlotte D. Slooter, Guilherme Macedo, Rodrigo Liberal, Ynto S. de Boer, Ana Lleo, N. van Gerven, K. van Erpecum, J den Ouden, J. Brouwer, J. Vrolijk, T.J. Gevers, J. Drenth, M. Guichelaar, G. Bouma, T.C.M.A. Schreuder, E.J. van der Wouden, L.C. Baak, P. Stadhouders, M. Klemt-Kropp, M. Verhagen, A. Bhalla, J. Kuijvenhoven, P. Almasio, F. Alvarez, R. Andrade, C. Arikan, D. Assis, E. Bardou-Jacquet, M. Biewenga, E. Cancado, N. Cazzagon, O. Chazouillères, G. Colloredo, M. Cuarterolo, G. Dalekos, D. Debray, M. Robles-Díaz, J. Drenth, J. Dyson, C. Efe, B. Engel, S. Ferri, R. Fontana, N. Gatselis, A. Gerussi, E. Halilbasic, N. Halliday, M. Heneghan, G. Hirschfield, B. van Hoek, M. Hørby Jørgensen, G. Indolfini, R. Iorio, P. Invernizzi, S. Jeong, D. Jones, D. Kelly, N. Kerkar, F. Lacaille, C. Lammert, B. Leggett, M. Lenzi, C. Levy, R. Liberal, A. Lleo, A. Lohse, S. Ines Lopez, E. de Martin, V. McLin, G. Mieli-Vergani, P. Milkiewicz, N. Mohan, L. Muratori, G. Nebbia, C. van Nieuwkerk, Y. Oo, A. Ortega, A. Páres, T. Pop, D. Pratt, T. Purnak, G. Ranucci, S. Rushbrook, C. Schramm, A. Stättermayer, M. Swain, A. Tanaka, R. Taubert, D. Terrabuio, B. Terziroli, M. Trauner, P. Valentino, F. van den Brand, D. Vergani, A. Villamil, S. Wahlin, H. Ytting, K. Zachou, M. Zeniya
Journal: Journal of Hepatology (2023)
Nondental Invasive Procedures and Risk of Infective Endocarditis: Time for a Revisit: A Science Advisory From the American Heart Association
Authors: Larry M. Baddour, Imre Janszky, Martin H. Thornhill, Zerelda Esquer Garrigos, Daniel C. DeSimone, Karen Welty-Wolf, Annette L. Baker, Pei-Ni Jone, Bernard Prendergast, Mark J. Dayer
Journal: Circulation (2023)

There have been no published prospective randomized clinical trials that have: (1) established an association between invasive dental and nondental invasive procedures and risk of infective endocarditis; or (2) defined the efficacy and safety of antibiotic prophylaxis administered in the setting of invasive procedures in the prevention of infective endocarditis in high-risk patients. Moreover, previous observational studies that examined the association of nondental invasive procedures with the risk of infective endocarditis have been limited by inadequate sample size. They have typically focused on a few potential at-risk surgical and nonsurgical invasive procedures. However, recent investigations from Sweden and England that used nationwide databases and demonstrated an association between nondental invasive procedures, and the subsequent development of infective endocarditis (in particular, in high-risk patients with infective endocarditis) prompted the development of the current science advisory.
Re: Robert J. Motzer, Pratik P. Rane, Todd L. Saretsky, et al. Patient-reported Outcome Measurement and Reporting for Patients with Advanced Renal Cell Carcinoma: A Systematic Literature Review. Eur Urol. Eur Urol. 2023;84:406–17
Authors: Andrés Felipe Gutiérrez Rojas, Daniel Fernández, Cesar Diaz Ritter
Journal: European Urology (2023)
Abstract Supplement ACR Convergence 2023
Authors: André Ramon, Hélène Greigert, Corentin Richard, Claudie Cladière, Coraline Genet, Marion Ciudad, Georges Tarris, Laurent Martin, Louis Arnould, Catherine Creuzot-Garcher, Paul Ornetti, Sylvain Audia, Romain Boidot, Jean-François Maillefert, Bernard Bonnotte, Maxime Samson
Journal: Arthritis & Rheumatology (2023)

For a searchable version of these abstracts, please visit www.acrabstracts.org.
Highlighted research articles
Journal: Cancer Discovery (2023)

In This Issue| October 05 2023 Highlighted research articles Author & Article Information Online ISSN: 2159-8290 Print ISSN: 2159-8274 ©2023 American Association for Cancer Research2023American Association for Cancer Research Cancer Discov (2023) 13 (10): 2109–2110. https://doi.org/10.1158/2159-8290.CD-13-10-ITI Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Article Versions Icon Versions Version of Record October 5 2023 Citation Highlighted research articles. Cancer Discov 1 October 2023; 13 (10): 2109–2110. https://doi.org/10.1158/2159-8290.CD-13-10-ITI Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest Search Advanced Search Cell-free DNA (cfDNA) concentrations in patients with cancer are often elevated. Mattox and colleagues sought to determine the source of this extra DNA by assessing cfDNA methylation patterns in 178 patients with cancers of the colon, pancreas, lung, or ovary as well as 64 patients without cancer. Leukocytes were found to contribute to the majority of cfDNA in nearly all samples regardless of total cfDNA concentration. The high levels of cfDNA observed in patients with cancer did not generally arise from neoplastic cells or from surrounding epithelial cells within the tumor. These data suggest that cancers may have a systemic effect on cell turnover or DNA clearance. See article, p. 2166. Breast cancer diagnosed postpartum (PPBC) is a malignancy with a poor prognosis that lacks effective screening protocols. In this study, Saura, Ortiz, and colleagues demonstrated the presence of cell-free tumor DNA (ctDNA) in the breast milk (BM) of... You do not currently have access to this content.
GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation
Authors: Bruno Contreras-Moreira, Shradha Saraf, Guy Naamati, Ana M. Casas, Sandeep S. Amberkar, Paul Flicek, Andrew R. Jones, Sarah Dyer
Journal: Genome biology (2023)

Abstract Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a species coding potential and link back to original annotations. The protocol get_pangenes performs whole genome alignments (WGA) to call syntenic gene models based on coordinate overlaps. A benchmark with small and large plant genomes shows that pangenes recapitulate phylogeny-based orthologies and produce complete soft-core gene sets. Moreover, WGAs support lift-over and help confirm gene presence-absence variation. Source code and documentation: https://github.com/Ensembl/plant-scripts .
MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases
Authors: Oren Ben-Kiki, Akhiad Bercovich, Aviezer Lifshitz, Ofir Raz, Dror Brook, Amos Tanay
Journal: Genome biology (2023)

We describe MCProj-an algorithm for analyzing query scRNA-seq data by projections over reference single-cell atlases. We represent the reference as a manifold of annotated metacell gene expression distributions. We then interpret query metacells as mixtures of atlas distributions while correcting for technology-specific gene biases. This approach distinguishes and tags query cells that are consistent with atlas states from unobserved (novel or artifactual) behaviors. It also identifies expression differences observed in successfully mapped query states. We showcase MCProj functionality by projecting scRNA-seq data on a blood cell atlas, deriving precise, quantitative, and interpretable results across technologies and datasets.
Generative modeling of living cells with SO(3)-equivariant implicit neural representations
Authors: David Wiesner, Julian Suk, Sven Dummer, Tereza Nečasová, Vladimír Ulman, David Svoboda, Jelmer M. Wolterink
Journal: Medical Image Analysis (2023)

Data-driven cell tracking and segmentation methods in biomedical imaging require diverse and information-rich training data. In cases where the number of training samples is limited, synthetic computer-generated data sets can be used to improve these methods. This requires the synthesis of cell shapes as well as corresponding microscopy images using generative models. To synthesize realistic living cell shapes, the shape representation used by the generative model should be able to accurately represent fine details and changes in topology, which are common in cells. These requirements are not met by 3D voxel masks, which are restricted in resolution, and polygon meshes, which do not easily model processes like cell growth and mitosis. In this work, we propose to represent living cell shapes as level sets of signed distance functions (SDFs) which are estimated by neural networks. We optimize a fully-connected neural network to provide an implicit representation of the SDF value at any point in a 3D+time domain, conditioned on a learned latent code that is disentangled from the rotation of the cell shape. We demonstrate the effectiveness of this approach on cells that exhibit rapid deformations (Platynereis dumerilii), cells that grow and divide (C. elegans), and cells that have growing and branching filopodial protrusions (A549 human lung carcinoma cells). A quantitative evaluation using shape features, Hausdorff distance, and Dice similarity coefficients of real and synthetic cell shapes shows that our model can generate topologically plausible complex cell shapes in 3D+time with high similarity to real living cell shapes. Finally, we show how microscopy images of living cells that correspond to our generated cell shapes can be synthesized using an image-to-image model.